The underlying hypothesis of our consortium is that host genes and networks involved in viral replication and in early host responses modulate viral pathogenesis and therefore represent targets for therapeutic intervention. In Project 2, we propose an OMICS approach to identify key early genes/networks involved in influenza virus pathogenesis. This will be achieved by modeling global host responses during influenza virus infection in a mouse model in collaboration with the Modeling Core E and the OMICs Cores B, C and D (Genomics, Proteomics and Metabolomics). In Aim 1, we will investigate the early global host response associated with lethal, severe and moderate influenza A virus infection in a mouse model. We will be using three clinically relevant strains of influenza A virus that differ in their virulence, allowing for comparisons of the host responses and interactions associated with different ranges of disease severity. In Aim 2, we will investigate host proteins interacting with influenza virus proteins during viral infection in mouse lungs, in collaboration with the Proteomics Core C, using the same influenza A virus strains as in Aim 1. The models constructed in collaboration with the Modeling Core E by the integration of the data generated in vivo with those ex vivo in Project 1 will predict key genes and networks likely to be involved in virus replication and host responses. In Aim 3, the model-identified networks will be validated by conducting perturbations including: use of specific virus mutants that disrupt key host-virus interactions, use of virus with specific mutations involved in host tropism and pathogenesis, use of pharmacological inhibitors, and use of mouse k.o. or of antisense targeting of key host genes in the mouse model. For antisense targeting in vivo we will be using a validated and innovative technology based on lung delivery of peptide-conjugated morpholino antisense oligomers (PPMO), pioneered by our collaborators Hong Mouton and David Stein. In all these experiments, viruses will be generated in collaboration with the Virus Core (Core G). In Aim 4, the results of these perturbations, approximately 40 per year, on the model networks will be analyzed in a medium throughput or targeted-OMICS approach, and the data will be incorporated into the model in collaboration with the Modeling Core E for model refinement. Targeted host genes in bur Project 2 will also be studied for variants and impact in human macrophage function by Project 3. We hypothesize that our integrated approach will result in the identification of novel host targets for therapeutic intervention during influenza virus infection.